Installation

IgDiscover is written in Python 3 and is developed on Linux. The tool also runs on macOS, but is not as well tested on that platform.

For installation on either system, we recommend that you follow the instructions below, which will first explain how to install the Conda package manager.

There are also non-Conda installation instructions if you cannot use Conda.

Installing IgDiscover in Conda environment

1. Install Conda by following the conda installation instructions as appropriate for your system. You will need to choose between a “Miniconda” and “Anaconda” installation. We recommend Miniconda as the download is smaller. If you are in a hurry, these two commands are usually sufficient to install Miniconda on Linux (read the linked document for macOS instructions):

   wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
   bash Miniconda3-latest-Linux-x86_64.sh
   

   When the installer asks you about modifying the PATH in your .bashrc file, answer yes.

2. Close the terminal window and open a new one. Then test whether conda is installed correctly by running

   conda --version
   

   If you see the conda version number, it worked.

3. Set up Conda so that it can access the bioconda channel. For that, follow the instructions on the bioconda website or simply run these commands:

   conda config --add channels defaults
   conda config --add channels bioconda
   conda config --add channels conda-forge
   

4. Clone the repository:

   git clone https://gitlab.com/gkhlab/igdiscover22.git
   cd igdiscover22
   

5. Bootstrap IgDiscover dependencies with this command:

   conda env create -f environment.yml -n igdiscover
   

   This will create a new so-called “environment” for IgDiscover (retry if it fails). Whenever you want to run IgDiscover, you will need to activate the environment with this command:

   source activate igdiscover
   

6. Install IgDiscover into Conda “environment” with command:

   pip install --no-deps -e ./
   

7. Make sure you have activated the igdiscover environment. Then test whether IgDiscover is correctly installed with this command:

   igdiscover --version
   

   If you see the version number of IgDiscover, it worked! If an error message appears that says “The ‘networkx’ distribution was not found and is required by snakemake”, install networkx manually with:

   pip install networkx==2.1
   

   Then retry to check the igdiscover version.

8. You can now run IgDiscover on the test data set to familiarize yourself with how it works.

Troubleshooting on Linux

If you use zsh instead of bash (applies to Bio-Linux, for example), the $PATH environment variable will not be setup correctly by the Conda installer. The miniconda installer adds a line export PATH=... to the to the end of your /home/your-user-name/.bashrc file. Copy that line from the file and add it to the end of the file /home/your-user-name/.zshrc instead.

Alternatively, change your default shell to bash by running chsh -s /bin/bash.

If you use conda and see an error that includes something like this:

ImportError: .../.local/lib/python3.5/site-packages/sqt/_helpers.cpython-35m-x86_64-linux-gnu.so: undefined symbol: PyFPE_jbuf

Or you see any error that mentions a .local/ directory, then a previous installation of IgDiscover is interfering with the conda installation.

The easiest way to solve this problem is to delete the directory .local/ in your home directory, see also how to remove IgDiscover from a Linux system.

Troubleshooting on macOS

If you get the error

ValueError: unknown locale: UTF-8

Then follow these instructions.

Development version

To install IgDiscover directly from the most recent source code, read the developer installation instructions.